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Background  Bacterial diarrhea is one of the most common causes for medical consultations, mortality and morbidity in the world. Diarrheagenic  Escherichia coli  (DEC) and non-typhoidal  Salmonella  (NTS) are major intestinal pathogens in developing countries, and the indiscriminate use of antibiotics has greatly contributed to resistant strains. Hence, the aim of the present study is to identify the antimicrobial resistance patterns and the molecular characteristics of DEC and NTS in southwest, China.    Methods  1121 diarrheal patients and 319 non-diarrheal subjects across all age groups were recruited from four sentinel hospitals from June 2014 to July 2015 in Kunming City, Yunnan Province. Each stool specimen was collected to detect DEC and NTS with standard microbiological and molecular methods. Antimicrobial resistance testing was performed with the Kirby-Bauer disk diffusion method, and the standards for antimicrobial susceptibility testing complied with the Clinical and Laboratory Standards Institute (CLSI). Molecular characterization of strains was carried out using pulsed-field gel electrophoresis (PFGE). A structured questionnaire was used to record basic epidemiological data (e.g. sex, age, residence, season, etc.). Data were analyzed using Chi-square or Fisher’s exact test.    Results  DEC was detected in 127 (11.33%) diarrhea cases and 9 (2.82%) non-diarrheal cases ( χ  2  = 20.69,  P  < 0.001,  OR  = 4.36, 95%  CI : 2.19–8.65), and the prevalence of NTS isolated from diarrhea cases was higher than that of non-diarrheal cases across all age groups ( n  = 42, 3.75%,  n  = 1, 0.31%,  χ  2  = 10.10,  P  = 0.002,  OR  = 12.38, 95%  CI : 1.70–90.29). The rates of resistance to ten antibiotics of DEC and NTS showed significant differences ( χ   2   = 386.77,  P  < 0.001;  χ  2  = 191.16,  P  < 0.001). The rates of resistance to Amoxicillin and Clavulafiate (AMC), Cephalothin (CEP), Gentamicin (GEN) and Sulfamethoxazole-Trimethoprim (SXT) of DEC isolated from diarrhea cases were higher than those of NTS isolated from diarrhea patients (37.01% vs 14.29%,  χ  2  = 7.57,  P  = 0.006; 29.92% vs 11.90%,  χ  2  = 5.40,  P  = 0.02; 37.01% vs 11.90%,  χ  2  = 5.80,  P  = 0.016; 62.20% vs 26.19%,  χ  2  = 16.44,  P  < 0.001; respectively). Ciprofloxacin (CIP) was the most sensitive antibiotic for DEC and NTS strains isolated from diarrhea cases. Resistance rates of DEC isolates from cases and controls to more than three kinds antimicrobials (multidrug resistance, MDR) showed no significant differences (81.10% vs 88.89%,  P  = 0.33). Pulsotype patterns of DEC strains were highly diverse; however, the pulsotype pattern of NTS strains was closely related to the serotype. The pattern of  S. enteritidis  was highly similar, but the  S. enterica  Typhimurium strain was discrete.    Conclusions  Antibiotic resistance of  Enterobacteriaceae  is of great concern. The societal effects of antibiotic use justify strict monitoring to combat increases in antimicrobial resistance. Molecular epidemiology and systematic epidemiological investigation can provide accurate evidence for tracking the infection source.    Electronic supplementary material  The online version of this article (10.1186/s40249-018-0427-2) contains supplementary material, which is available to authorized users.

infectious diseases of poverty

Antibiotic resistance and molecular characterization of diarrheagenic Escherichia coli and non-typhoidal Salmonella strains isolated from infections in Southwest China